5JJV

Crystal structure of XerH site-specific recombinase bound to palindromic difH substrate: post-cleavage complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural snapshots of Xer recombination reveal activation by synaptic complex remodeling and DNA bending.

Bebel, A.Karaca, E.Kumar, B.Stark, W.M.Barabas, O.

(2016) Elife 5: --

  • DOI: 10.7554/eLife.19706
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterial Xer site-specific recombinases play an essential genome maintenance role by unlinking chromosome multimers, but their mechanism of action has remained structurally uncharacterized. Here, we present two high-resolution structures of Helicoba ...

    Bacterial Xer site-specific recombinases play an essential genome maintenance role by unlinking chromosome multimers, but their mechanism of action has remained structurally uncharacterized. Here, we present two high-resolution structures of Helicobacter pylori XerH with its recombination site DNA difH, representing pre-cleavage and post-cleavage synaptic intermediates in the recombination pathway. The structures reveal that activation of DNA strand cleavage and rejoining involves large conformational changes and DNA bending, suggesting how interaction with the cell division protein FtsK may license recombination at the septum. Together with biochemical and in vivo analysis, our structures also reveal how a small sequence asymmetry in difH defines protein conformation in the synaptic complex and orchestrates the order of DNA strand exchanges. Our results provide insights into the catalytic mechanism of Xer recombination and a model for regulation of recombination activity during cell division.


    Organizational Affiliation

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine recombinase XerH
A, B
363Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Gene Names: xerH
Find proteins for O25386 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  O25386
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*GP*TP*TP*AP*TP*GP*AP*AP*AP*AP*C)-3')C,E13Helicobacter pylori 26695
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*CP*AP*GP*TP*TP*TP*TP*CP*AP*TP*AP*AP*CP*TP*A)-3')D,F17Helicobacter pylori 26695
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.195 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 86.380α = 90.00
b = 115.220β = 90.00
c = 235.200γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
autoSHARPphasing
XDSdata scaling
PHENIXmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-04-25 
  • Released Date: 2016-12-28 
  • Deposition Author(s): Bebel, A., Barabas, O.

Revision History 

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2017-01-11
    Type: Database references
  • Version 1.2: 2018-09-19
    Type: Advisory, Data collection, Database references